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Identification and sequence analysis of a DREB subfamily transcription factor involved in drought stress tolerance from rice

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DRE (dehydration responsive element)/CRT (C-repeat) is a cis-acting element that involves in gene expression responsive to abiotic stress in higher plants. To date, all well known DREBP transcription factors in Arabidopsis, rice, maize and other plants regulate gene expression in response to drought, high-salt and cold stresses by binding specifically to DRE/CRT. Using a target sequence of 50 nucleotides on Glutamate dehydrogenase-like protein (JRC2606) promoter containing the core sequence of DRE cis-acting element (A/GCCGAC) for yeast one-hybrid screening, we have identified two transcription factors: a completely homology of OsRAP2.4A gene and another is a new sequence. The new sequence contained an ORF (Open Reading Frame) of 1017-bp and 5’ non-coding area of 35-bp and 3’ non-coding area of 341-bp. The deduced amino acid sequence contains an AP2 domain and belongs to the subgroup A6 of DREB subfamily, temporarily named OsRAP2.4B. Sequence alignment showed that OsRap2.4B had homology with ZmDBF, a maize transcription factor involved in drought stress tolerance.

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74

Identification and Sequence analysis of a DREB

subfamily transcription factor involved

in drought stress tolerance from rice

Xuan Hoi Pham, Tuan Tu Tran

The Institute of Agricultural Genetics, Hanoi

Abstract: DRE (dehydration responsive element)/CRT (C-repeat) is a cis-acting element that involves

in gene expression responsive to abiotic stress in higher plants To date, all well known DREBP

transcription factors in Arabidopsis, rice, maize and other plants regulate gene expression in response to

drought, high-salt and cold stresses by binding specifically to DRE/CRT Using a target sequence of 50 nucleotides on Glutamate dehydrogenase-like protein (JRC2606) promoter containing the core sequence of

DRE cis-acting element (A/GCCGAC) for yeast one-hybrid screening, we have identified two transcription factors: a completely homology of OsRAP2.4A gene and another is a new sequence The new sequence

contained an ORF (Open Reading Frame) of 1017-bp and 5’ non-coding area of 35-bp and 3’ non-coding area of 341-bp The deduced amino acid sequence contains an AP2 domain and belongs to the subgroup

A6 of DREB subfamily, temporarily named OsRAP2.4B Sequence alignment showed that OsRap2.4B had homology with ZmDBF, a maize transcription factor involved in drought stress tolerance

Keywords: Transcription factor, DRE/CTR, OsRap2.4B, drought stress tolerance

Plants are not mobile and thus must respond

and adapt to abiotic stress such as drought, high

salt, heat, cold in order to survive Under these

stresses, plants induce various biochemical and

physiological changes in process of acquiring

stress tolerance Discovering of numerous genes

responsible for stress tolerance suggests that

many of them are transcription factors [16]

Among these transcription factors is an

ERFBP/AP2 family has been identified in a

variety of higher plants Significantly, the

introduction of many stress-inducible genes via

gene transfer resulted in improved plant stress

tolerance [16, 17, 19] In Arabidopsis, this

family consists of 145 distinct genes encoding

ERFBP/AP2 protein and can be divided into

three subgroups based on the number of

ERFBP/AP2 domains in each molecule The

AP2 subgroup includes 14 genes, each encodes

a protein containing two ERFBP/AP2 domains

The RAV subgroup includes six genes that

conserve two different DNA-binding domains,

ERFBP/AP2 and B3 The ERFBP subgroup

includes 125 genes, each encodes a protein with

only one ERFBP/AP2 domain Of these, 121

genes contain a conserve WLG motif in the

middle of their ERFBP/AP2 domain [15] The

members of the ERFBP subgroup can be further divided into two subfamilies: DREB subfamily and DREB-like protein subfamily, based on the similarity of the amino acid sequence of the DNA-binding domain DREB subfamily

consists of 56 genes in Arabidopsis genome and

all of them contain one ERFBP/AP2 domain considered to play a crucial role in the process

of the response to environmental stresses DREB subfamily is divided into 6 small groups based

on similarities of the binding domain The first and second small groups (A1, A2) include of DREB1/CBF and DREB2 gene families, respectively The third small group (A3) has only ABI4 The fourth small group (A4) contains 16 genes, including TINY The fifth small group (A5) consists of 16 genes, including RAP2.1, RAP2.9 and RAP2.10 The sixth small group (A6) consists of nine genes, including RAP2.4 [15]

DREB subfamily specifically recognizes and binds to the dehydration responsive element

(DRE) or DRE-like cis-element The core

sequence of the DRE is A/GCCGAC that exists frequently in promoters of plant genes induced

by dehydration, high salt, heat and cold stresses

[18] Both DRE-like cis-elements, named

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C-repeat (CRT) and low-temperature-responsive

element (LTRE) contained a CCGAC core motif

also reported to regulate low-temperature

inducible promoters [1, 9]

DREB subfamily so far includes

DREB1A-C (DREB1A-CBF1-3), DREB2A-B, three novel DREB1s

and six novel DREB2-related genes in

Arabidopsis genome have been isolated, and

their corresponding gene products showed

significant sequence similarity to the conserved

DNA-binding domain found in ERFBP/AP2

proteins [8, 11, 15] Expression of the

DREB1/CBF genes induced by cold stress and

their gene products activate the expression of

more than 40 genes in the DREB1/CBF region

and resulted in an improved tolerance not only

to freezing but also to drought and high salinity

[3] DREB1/CBF orthologs have been reported

and shown to functional in cold stress tolerance

from various species, including Brassica napus,

tomato, barley, maize, rice, and wheat [2, 4-7,

13] In contrast, expression of the DREB2

genes induced by dehydration or high salt stress

rather than cold stress Overexpression of

DREB2A in transgenic plants does not activate

downstream genes under normal growth

condition suggesting that post-translational

regulation may be involved in its activation [11]

Recently, a negative regulatory domain

identified in central region of DREB2A and

deletion of this region transforms DREB2A to a

constitutive active form, DREB2A CA

Transgenic Arabidopsis overexpression

DREB2A CA showed increased expression of

many stress inducible genes and resulted in an

improved tolerance to drought stress [14] A

number of efforts have been focused on

characterization of drought and high-salt stress

transcription factors in different plants including

rice, wheat, barley and maize [2, 13] However,

function of these genes under drought condition

is not much clear, except ZmDREB2A that is

accumulated by cold, dehydration, salinity and

heat stresses Unlike DREB2A, ZmDREB2A

produced two forms of transcripts but only

functional transcription form of ZmDREB2A

significantly induced by stresses suggesting that

protein modification is not necessary for

ZmDREB2A function Transgenic plants

overexpressing ZmDREB2A resulted in up

regulation expression of a number of drought inducible genes including late embryogenesis abundant (LEA), heat shock and detoxification proteins Constitutive or stress-inducible

expression of ZmDREB2A resulted in an

improved drought stress tolerance in plant [13]

I Materials and Methods

1 Plant materials and stress treatments

An Indica rice variety namely cultivar Moc tuyen was grown in controlled conditions in incubator at 30 ± 1oC and 12 h photoperiod The seeds were first soaked in water at room temperature overnight and surface sterilized by bovastin powder for 15 min and after that kept under following water for half an hour To germinate, seeds kept on autoclaved germination paper (at a distance app 1cm between seeds), rolled and kept into beaker Half strength MS basal medium (liquid) supplied after seeds germinated After ten days, drought treatments given by putting them into 20% PEG solution for

1, 4, 8 and 24 h; all of them were collected separately put in liquid nitrogen and stored at

-80oC till the further use

2 Construction of stress cDNA library

Total RNA extracted from 15-day-old rice using GITC buffer standard protocol The mRNA was purified from total RNA by magnetic separation after annealing with biotinylated oligo-dT primer and immobilizing

it onto streptavidin-linked paramagnetic beads

cDNA Library was constructed from 5 µg of mRNA in Hybrid Zap 2.1 vector by following manufacturer’s (Stratagene) protocol using HybriZAP-cDNA library Synthesis Kit (HybriZAP®-2.1 XR Library construction kit and HybriZAP®-2.1 XR cDNA synthesis kit, http://www.stratagene.com/manuals/235612.pdf) The resulting cDNA was unidirectional

subcloned into EcoRI and XhoI sites within the

MCS region in the phage vector, and packaged

by Gigapack III Gold packaging extract After amplification primary library according manufacturer’s protocol, phage library were aliquot into eppendorf tubes and stored at -80oC for long time The titer of the cDNA library is estimate around 1010 pfu/ml after amplifying (data not show) After that, pAD-GAL4 2.1

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76

vector was excised from the Hybrid Zap 2.1

vector according to mass in vivo excision

protocol from Stratagene (data not shown)

3 Construction of reporter plasmids for

yeast one-hybrid screening

We have selected target sequences contain

DRE sequences from a promoter sequence of a

cold stress-inducible gene encoding glutamate

dehydrogenase-like protein (JRC2606) Specific

target sequence is AGCCAAACGCAGCCG

GCCGACCTCCTCCCGTGCCTTCCTCCTCGA

TCCCC The pHISi-1 and pLacZi vectors are

employed for constructing target-reporter

constructs

4 Yeast one-hybrid screening of rice

drought cDNA library

Dual reporters of pHISi-1 and pLacZi

containing four tandem copies of target

sequences were linearized by XhoI and NcoI

respectively, then transformed into Yeast genome (YM4271, Clontech) to form parental yeast containing both reporters Yeast one-hybrid screening of rice drought cDNA library was carried out as manual protocol of yeast one

hybrid screening (Clontech) These clones were

isolate with yeast DNA isolation protocol of Clontech pAD-GAL4 plasmids containing cDNA inserts were isolated from the positive clones After that cDNA were excised with

Eco RI from pAD-GAL4 plasmid and then ligated into pSK II vector for sequencing

II Results

1 Isolation of cDNA encoding DNA binding proteins that interact with DRE in the

50-bp DNA fragment of JRC2606 promoter

Figure 1. Design and construction of target sequence Electrophoresis PCR produce with specific primer T7/T3 show that lane 7 and 8 are emty vector; lane 3 and 4 are vector containing a insert DNA including 2 tandem repeated target sequences Similarry lane 6, lane 9/10 are the PCR produce of a vector containing 4 and 6 tandem repeated target sequence, respectively The clone sixth was chosen for isolating plasmids and sequencing The result also comfirm that this clone containing a vector with 4 tandem repeated target sequence be beatwen Sma I and EcoR I sitr in the MCS region

To isolate cDNA encoding DNA binding

proteins that interact with DRE motif, we have

used yeast one-hybrid screening system The

first, we synthesized three pair of antiparallel

oligo-nucleotides of the target sequence In each

pair, one strand represents the sense and the

other its antisense complement The sense

strand of first pair of antiparallel

oligo-nucleotides containing EcoRI site in 5’ end

anneals with its antisense to form fragment 1

The second pair of antiparallel oligo-nucleotides containing 10 nucleotides tails in both 3’ ends forms fragment 2, since it can be self-ligated to extend copy number The sense strand of the third pair of antiparallel oligo-nucleotides

containing SmaI site in 3’ end anneals with its antisense containing SmaI site at 5’ end to form

fragment 3 (fig 1A) In principle, fragments 1,

2 and fragments 3 have 10 nucleotides overlap, therefore fragments 1, 2 and 3 can anneal to

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form a sequence containing at least three

tandem repeat target sequences by T4 ligase

(Fig 1a) Then the ligated DNA was cloned in

pSKII vector by EcoRI/SmaI sites The

sequences cloned in pSKII vector has checked

by electrophoresis on agarose gel 1% (fig 1B)

and rechecked again on sequencer ABI (3100)

After that, the sequence was excised and cloned

into vectors pHISi-1 and pLacZi, by

Eco RI/SmaI sites (fig 1A) The number copies

of target sequences in reporter vectors pHISi-1

and pLacZi were re-confirmed by sequencing and then transformed into yeast genome Following this strategy, we obtained a parental yeast strain containing as dual reporter genes

integrated copies of HIS and LacZ with

four-time tandem repeated 50-bp DNA fragments of JRC2606 promoter The resulting parental yeast

strain transcribes the HIS3 gene at basal levels,

grows on media lacking histidine and forms the blue colonies on the filter paper containing X-gal

Figure 2 The basal expression level of HIS3 and LacZ genes of parental Yeast

on the medium SD/-His/-Ura The second, we discovered the basal

expression level of HIS3 and LacZ genes of

parental Yeast by growing the yeast strain on

SD/-His/-Ura plates containing different

concentration of 3-aminotriazole (3-AT, an

inhibitor of the HIS3 gene product) and β-

glactosidase filter assay respectively For basal

expression level of HIS3 gene, we found that

parental yeast till grew weakly on SD/-His/-Ura

plates containing 7.5 mM 3-AT but did not

grow on SD/-His/-Ura plates containing 10 mM

3-AT (fig 2) For basal expression level of LacZ

gene, we found that filter turned blue in IPTG

and X-gal media after 30 minutes (fig 2)

The parental yeast cells transformed with

drought cDNA library from a mix of rice plants

dehydrated for 1, 4, 8 and 24 hours If target

gene encoding transcription factor that can

recognize the binding site (DRE) and like a transcriptional activator of the reporter genes it allows the recombinant yeast cells to grow in the presence of 10 mM 3-AT and filter in β-glactosidase assay turned blue before 30 minutes

Screening of 1.5 × 106 recombinant yeast cells, we have obtained 28 positive clones that grown on SD/-His/-Ura/-Leu containing 10 mM 3-AT and filter in β-glactosidase assay turned blue before 20 minutes Re-screening 28 positive clones on SD/-His/-Ura/-Leu containing

50 mM 3-AT, 12 positive clones have grown normally on this medium The cDNA of these

12 chosen clones were isolated from yeast cells and subjected for sequencing

2 Sequence and structural analysis of an

DREB subfamily, OsRap2.4B

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78

To identify these positive clones, 12 positive

clones were sequenced by ABI sequencer version

3100 The sequencing data revealed that, five

positive clones completely match in sequence

with each other’s, four positive clones completely

match with other sequence and remained positive

clones are not match in sequence The aligment

DNA of sequences with rice genome showed that

the group of five positive clones is OsRap2.4A

(sequence is not shown), the other group of four

positive clones is a new sequence temporary

named OsRap2.4B (fig 3) The OsRap2.4B

cDNA contained an ORF (Open Reading Frame)

of 1017-bp and 5’ non-coding area of 35-bp and 3’ non-coding area of 341-bp Its deduced 339 amino acid sequence indicated that this protein with predicted molecular mass of 38 kDa contains an AP2 domain of 59 amino acids and a WLG motif localized in central of AP2 domain (fig 3)

1 ttgccatcttcatcttctacctccatccagtcctcATGGCCGCAGCAATAGACATGTACA 61

M A A A I D M Y K

61 AGTATAACACTAGCACACACCAGATCGCATCCTCGGATCAGGAGCTCATGAAAGCGCTCG 121

Y N T S T H Q I A S S D Q E L M K A L E

121 AACCTTTTATTAGGAGCGCTTCTTCTTCCTCCGCTTCCTCCCCCTGCCACCACTACTACT 181

P F I R S A S S S S A S S P C H H Y Y S

181 CTTCTTCTCCTTCCATGAGCCAAGATTCTTACATGCCCACCCCATCTTATCCCACTTCCT 241

S S P S M S Q D S Y M P T P S Y P T S S

241 CTATCACAACCGCCGCCGCCACCACCACCTCGTCTTTCTCGCAGCTACCTCCGCTGTACT 301

I T T A A A T T T S S F S Q L P P L Y S

301 CTTCGCAGTATCATGCTGCTTCACCTGCGGCGTCGGCGACGAACGGGCCGATGGGGCTGA 361

S Q Y H A A S P A A S A T N G P M G L T

361 CCCACCTGGGCCCAGCCCAGATCCAGCAGATCCAGGCCCAGTTCTTGGCCCAGCAGCAGC 421

H L G P A Q I Q Q I Q A Q F L A Q Q Q Q

421 AGCAGAGGGCCCTGGCCGGCGCCTTCCTTCGGCCGCGTGGCCAGCCGATGAAGCAGTCCG 481

Q R A L A G A F L R P R G Q P M K Q S G

481 GGTCGCCGCCGCGCGCGGGGCCGTTCGCGGCGGTCGCCGGGGCGGCGCAGTCGAAGCTCT 541

S P P R A G P F A A V A G A A Q S K L Y

541 ACCGCGGAGTGCGGCAGCGCCACTGGGGGAAGTGGGTGGCGGAGATCCGCCTCCCGAAGA 601

601 ACCGGACGCGGCTGTGGCTCGGCACCTTCGACACCGCCGAGGACGCCGCGCTCGCCTACG 661

661 ACAAGGCCGCCTTCCGCCTCCGCGGCGACCTCGCGCGGCTCAACTTCCCCACCCTCCGCC 721

721 GCGGCGGCGCCCACCTCGCCGGCCCGCTCCACGCCTCCGTCGACGCCAAGCTCACCGCCA 781

781 TCTGCCAGTCCCTCGCCACGAGCTCGTCCAAGAACACCCCCGCCGAGTCAGCGGCCTCCG 841

841 CGGCGGAGCCGGAGTCCCCCAAGTGCTCGGCGTCGACGGAAGGGGAGGACTCGGTGTCCG 901

901 CCGGCTCCCCTCCTCCGCCCACGCCGCTGTCGCCCCCGGTGCCGGAGATGGAGAAGCTGG 961

961 ACTTCACGGAGGCGCCATGGGACGAGTCGGAGACATTCCACCTGCGCAAGTACCCGTCCT 1021

1021 GGGAGATCGACTGGGACTCAATCCTCTCATAAacaagcagaagcagctactactagtcta 1081

E I D W D S I L S s.codon

1081 ttactagtactagtagtagtcttcgtcaagctagagtcactcaactcaactagctgtgta 1141

1141 atcttctctgaattccgtggcttccatggctcggtggcattttagacgtcggccatggct 1201

1201 gctgcgagtagcagtaactagtcagtactcagtagtagtaaggtcgttggtattacgtcg 1261

1261 tcgtgcaagtgtcgttggtgtactcagtgatctgatctcctggttgagctgccggttgtt 1321

1321 tttttcacggcgcggccggtcgagaattaagctgtaatcccttgttacatgttggaaatt 1381

1381 cagtagcttatgt 1393

Figure 3 Nucleotide and deduded amino acid sequence of cDNA temporary named OsRap2.4B

In order to clarify the relationship of

OsRap2.4B in the super family of ERF/AP2

transcription factor in plants A systematic

phylogenic analysis of the ERF/AP2 domains of

these proteins was based on the classification of

121 ERF/AP2 transcription factors in

Arabidopsis [15] We have analyzed the

similarities of OsRap2.4B with protein from

other species including Arabidopsis, rice and

revealed that it belongs to A-6 subgroup of

DREB subfamily (fig 4)

In addition, sequence alignment of

OsRap2.4B and homolog DREB subfamily transcription factors from different species

shown that OsRap2.4B had striking homology with Rap2.4, OsRap2.4A and ZmDBF1

respectively In detail, OsRap2.4B has

maximum of 76% identity with Rap2.4, 67% with OsRap2.4A and 51% with ZmDBF1 There

is not much homology on over the entire length

of the amino acid sequence between these

Trang 6

proteins However, a striking homology on a

region of 59 amino acids (AP2 domain) and

WLG motif localization in central of AP2

domain were observed among these proteins

Beside, before the AP2 domain, two conserved

sequences (QA/SQ, Q/LP/LMKPP/QA/S) like motif presented and after the AP2 domain, there are another two basic regions in C-terminal region These sequences might act as an activation domain for transcription (fig 5)

OsDREB1J

A6

RAP 2.4 B

Figure 4 Phylogenic tree of OsRap2.4B built by Cluster

Figure 5 Alignment deduced amino acid sequences of OsRap2.4B with other similarly homology genes in A6 subgroup of DREB subfamily by Genetyx 6.0 The result show that OsRap2.4B have a

strictly homology with the rest in AP2 domain and the present of WLG

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80

III Discussion

DREBP subfamily bind to DRE or DRE like

cis -element and regulate expression of stress

inducible genes has been accurately determined

at molecular level However, all of these studies

were focused on DREB1 and DREB2 and

homolog genes [16, 19], except ZmDBFs [10]

We have identified a new transcription factor,

OsRap2.4B that belongs to A6 subgroup The

deduced amino acid sequence of OsRap2.4B

contained an AP2 DNA binding domain of 59

amino acids and WLC motif localization in

central of AP2 domain, which were conserved in

all the other DREB subfamily transcription

factors [15] DRE - binding activity as well as

functions of transcription factors belong to A6

subgroup has not been determined at molecular

level yet

However, at least five DREBP subfamily

transcription factors: DREB1,2, OsDREB1,

Zm DREB1 and ZmDBF1 have been isolated by

yeast one-hybrid screening and all of them

contained DRE-binding activity [10-13] Yeast

one hybrid screening using a target sequence of

50 nucleotides containing DRE sequence

suggesting that the new sequence identified

OsRap2.4B did binding to DRE sequence Two

new DRE-binding proteins, DBF1 and DBF2 are

members of the AP2/EREBP transcription factor

family that bound to the wild-type DRE2 element

and regulated expression of stress inducible

genes and resulted in an improve drought

tolerance in transgenic plants [10] Sequence

alignment of OsRap2.4B and homolog DREB

subfamily transcription factors from different

species showed OsRap2.4B striking homology

with Rap2.4, OsRap2.4A and ZmDBF1,

indicating this transcription factor may also have

functions in common with ZmDBF1 and improve

drought tolerance in transgenic plants A futher

study on function analysis of OsRap2.4 will

come out soon

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Phân lập và phân tích trình tự gien m+ hóa nhân tố phiên m+ thuộc phân nhóm DREB ở lúa liên quan đến tính chịu hạn

Phạm Xuân Hội, Trần Tuấn Tú

Tóm tắt

DRE (yếu tố/đoạn C lặp lại đáp ứng hạn) là trật tự ADN đặc hiệu trên vùng điều khiển hoạt động gien liên quan đến biểu hiện các gien đáp ứng với các điều kiện bất lợi ngoại cảnh ở thực vật Tất cả các yếu tố phiên

mb được nghiên cứu chi tiết đặc tính ở cây mo hình Arabidopsis, lúa, ngô và các thực vật khác điều khiển biểu

hiện các gien đáp ứng với điều kiện hạn, mặn và lạnh thông qua việc bám đặc hiệu vào trình tự DRE/CRT Sử

dụng trật tự ADN đích gồm 50 nucleotit trên vùng điều khiển hoạt động gien Glutamate dehydrogenase-like

protein (JRC2606) chứa trình tự ADN đặc hiệu DRE cho việc sàng lọc (yeast one hybrid screening), chúng tôi

phân lập được hai nhân tố phiêm mb thuộc tiểu nhóm A6 của phân nhóm DREB và đặt tên là OsDREB2.4A và

OsDRE2.4B Trật tự cDNA của OsDREB2.4B có vùng mb hoá là 1017-bp, vùng không mb hóa gen đầu 5’ là 35-bp và vùng không mb hóa gien đầu 3 ’ là 341 cặp bazơ Phân tích trình tự amino acid của gien OsDREB2.4B

cho thấy có chứa vùng hoạt động AP2 So sánh sự tương đồng về trình tự amino acid được mb hoá bởi gien OsDREB2,4B với các nhân tố phiên mb thuộc phân nhóm DREB của các đối tượng cây trồng khác nhau cho

thấy gien OsDREB2.4B tương đồng với nhân tố phiên mb ZmDBF ở ngô Nhân tố phiên mb ZmDBF ở ngô tăng cường tính chịu hạn ở thực vật vì vậy nhân tố phiên mb OsDRE2.4B chúng tôi mới phân lập được có thể

tăng cường tính chịu hạn ở thực vật

Ngày nhận bài: 12-11-2008

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